City had to wait 71 minutes for a shot on target – resulting in Erling Haaland’s opening goal – as a well-organised Everton defended deep and gave away few opportunities.
The Blues’ boss says he also expected nothing less against an Everton side who are never easy to play against.
“I love to win this type of game,” said Pep.
“The difficulty is there, we knew it. Everton at home is always complicated. We lost a lot of points over the years.
“What I am happy with the most was the shape and the body language in the second half was much better.
“The first half we were complaining. 12:30 kick-off is more difficult, but the body language was not good.
“The chemistry between the players, we have to better, in the second half we were better.
“We read better, the space we should attack. Kyle, Kevin, Bernardo, and Jack made an incredible contribution - especially Jack in the last minutes, to keep the ball.
“I like to win these games suffering. How difficult it is in the Premier League. Nothing is for granted.
“The way they celebrate shows how difficult it was and how pleased they are.”
The second of Haaland’s brace came after a threaded pass from Kevin De Bruyne as the pair combined for a goal for the first time this season.
Guardiola says both players have qualities each other need and their return will only strengthen his team’s bid for more silverware.
“Since day one, Kevin needs runners and the runner off Kevin needs assists,” he said.
“There was a connection in a natural way. Kevin is back, Erling is back and it’s so important for us. The first goal was so difficult. I’m really pleased.”
The City boss also admitted a different tactic involving his full-backs coming into midfield didn’t go as planned and a change was needed.
“We tried but it didn’t work,” Pep admitted.
“Manu (Akanji) didn’t feel comfortable. We changed our structure. We didn’t read where the space was.
“The space was with Phil and Jeremy. We didn’t use the middle to go to the opposite side.
“It’s similar to Goodison Park, we changed our rhythm like today. Hopefully next season we start better against them.”